[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the jupyterlab/jupyterlab codebase. Here's the problem: Add watch handling for non-symlinked dynamic extensions <!-- Welcome! Thanks for thinking of a way to improve JupyterLab. If this solves a problem for you, then it probably solves that problem for lots of people! So the whole community will benefit from this request. Before creating a new feature request please search the issues for relevant feature requests. --> ### Problem Extensions that are installed with `labextension develop` without a symlink currently do not support `watch` mode. <!-- Provide a clear and concise description of what problem this feature will solve. For example: * I'm always frustrated when [...] because [...] * I would like it if [...] happened when I [...] because [...] --> ### Proposed Solution - When we call `labextension watch`, check for a `symlink` to the watched directory. If none exists, check for a `labextensions` directory. If none exists, bail. If there is a `labextensions` directory, set up file system watchers to copy changes to that location from the `src` directory of the extension in addition to running the local `watch` command. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conda/conda codebase. Here's the problem: CondaError: Cannot link a source that does not exist. C:\Users\...\Anaconda3\Scripts\conda.exe I get this error when trying to conda install tqdm. Pip install works fine. However, when trying conda install spacy, I still get the same error because the conda installation for spacy attempts to conda install tqdm. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the jupyterlab/jupyterlab codebase. Here's the problem: Split the repository into multiple packages This issue signals the intent to split the repository up into multiple packages in the same repository, following the example of [phosphor](https://github.com/phosphorjs/phosphor). Having independent packages allows them to be separately required by downstream consumers. It is also a required step to enable plugin bundles to contain the entire package that they require, allowing us to treat each package as a unit when de-duplicating the final bundle. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: Pubsub API redesign broke support for PUBSUB_EMULATOR_HOST Broke 2 days ago with this diff: https://github.com/GoogleCloudPlatform/google-cloud-python/commit/4a8e155c0e85bf80edbf2e5f1e9342bc3f571acb#diff-c15e14c96ae7c1e14ebdff735c3080e6L62 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: Make storage ACL objects handle lazy loading and remove get_acl() from Key / Bucket See #333 Make storage ACL objects handle lazy loading and remove get_acl() from Key / Bucket See #333 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the numpy/numpy codebase. Here's the problem: Improve performance of tril_indices and triu_indices <!-- Please describe the issue in detail here, and fill in the fields below --> `tril_indices` and `triu_indices` uses `nonzero` to get the indices. np.nonzero seems rather slow compared to other methods I've tested. ### Reproducing code example: <!-- A short code example that reproduces the problem/missing feature. It should be self-contained, i.e., possible to run as-is via 'python myproblem.py' --> ```python import numpy as np def tril_indices(n, k=0, m=None): tri = np.tri(n, m, k=k, dtype=bool) return tuple(np.broadcast_to(inds, tri.shape)[tri] for inds in np.indices(tri.shape, sparse=True)) def triu_indices(n, k=0, m=None): tri = ~np.tri(n, m, k=k - 1, dtype=bool) return tuple(np.broadcast_to(inds, tri.shape)[tri] for inds in np.indices(tri.shape, sparse=True)) %timeit np.tril_indices(500) 2.14 ms ± 52.9 µs per loop (mean ± std. dev. of 7 runs, 100 loops each) %timeit tril_indices(500) 684 µs ± 60.1 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each) ``` ### NumPy/Python version information: <!-- Output from 'import sys, numpy; print(numpy.__version__, sys.version)' --> `print(np.__version__, sys.version)` 1.17.5 3.7.9 (default, Aug 31 2020, 17:10:11) [MSC v.1916 64 bit (AMD64)] Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Lightning-AI/lightning codebase. Here's the problem: Wandb Group Argument ## 🚀 Feature Wandb currently supports an argument group to its init function that is not currently exposed by the PL api. I was hoping that we could expose this argument to the user to pass into the wandb init call. ### Motivation This would allow users to group their experiments on the wandb platform and keep them ordered together. ### Pitch Add an argument to the wandb logger, pass this into the wandb init call. ### Additional context https://docs.wandb.com/library/init Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: gate.control() Enhance the Gate class with a method for controlling it. This should return a new `ControlledGate` (which derives from `Gate`). - [x] Implement `ControlledGate` class. Existing controlled gates such as CX and CH and CSWAP and CCX should derive from this now. (#2862) After this implementation, the following should work: ```python # inst is a 2 qubit instruction # circ is a 5 qubit circuit circ.append(inst.q_if(), [0, 2, 1]) circ.append(inst.q_if(2), [0, 3, 1, 2]) circ.append(inst.q_if().q_if(), [0, 3, 1, 2]) # should be same as above circ.draw() # should clearly show controlled gates circ.decompose() # should decompose the controlled gates one level ``` Follow ups: - [x] Expose in a nicer user interface. - [ ] Write transpiler passes that efficiently use ControlledGate. notes: 1- `control` currently clashes with a property of the instruction. So let's use the `q_if` method for now, with the goal of eventually moving to `control`. 2- The decomposition should be shallow, in the sense that the controlled gate provides a definition only in terms of controlling its subcomponents. It will be the job of the unroller to take this definition recursively until the end and implement a circuit over U3 and CX. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: pulse builder measure cannot handle multiple qubits <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues --> ### Information - **Qiskit Terra version**: - **Python version**: - **Operating system**: ### What is the current behavior? A code inserts multiple `pulse.measure` instruction creates strange output. ![image](https://user-images.githubusercontent.com/39517270/88929910-ba9d3580-d2b5-11ea-832e-999ff6593960.png) ### Steps to reproduce the problem ```python from qiskit import pulse with pulse.build(backend) as sched: with pulse.align_left(): for i in range(5): pulse.measure(i) ``` ### What is the expected behavior? All measure and acquire instructions are aligned in parallel. ### Suggested solutions This is a defect arising from the constraints of IQX backends measurement operation. Currently it inserts the acquire instruction for all qubits while a measurement pulse is inserted for the specific qubit. Thus repeating `pulse.measure` occupies timeslots of other acquire channels and they cannot be aligned. This issue will be automatically solved when the acquisition for single qubit is supported by backend, or we can temporarily solve this by allowing iterator as `qubit` argument. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conan-io/conan codebase. Here's the problem: [feature] Provide conan.tools.microsoft.msvs_toolset equivalent of conans.tools.msvs_toolset Would it be possible to provide the [msvs_toolset](https://docs.conan.io/en/latest/reference/tools.html#tools-msvs-toolset) function in the `conan` namespace and add support for the `msvc` compiler in it? I had to workaround the use of the original `msvs_toolset` function in my recent update to the Boost recipe in conan-io/conan-center-index#12819. - [X] I've read the [CONTRIBUTING guide](https://github.com/conan-io/conan/blob/develop/.github/CONTRIBUTING.md). Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: DEBUG log messages emitted on imports ### Environment - **Qiskit Terra version**: main (but previous release likely also have the issues - **Python version**: 3.10 - **Operating system**: Linux ### What is happening? When importing some modules, including the root `qiskit` namespace, `DEBUG` log messages get emitted. For example `import qiskit` emits: ``` DEBUG:qiskit.quantum_info.synthesis.two_qubit_decompose:Requested fidelity: None calculated fidelity: 1.0 actual fidelity 0.9999999999999997 ``` and `import qiskit.test` emits: ``` DEBUG:qiskit.test.testing_options:{'skip_online': False, 'mock_online': False, 'run_slow': False, 'rec': False} ``` ### How can we reproduce the issue? ```python3 import logging logging.basicConfig(level="DEBUG") import qiskit ``` ### What should happen? We shouldn't be emitting runtime log messages during an import. This is primarily a side effect of code being executed at the module level on import, normally to setup global objects, but emitting these log messages on import is missing the context and really serves no useful purpose. ### Any suggestions? First we need to find all the places this is happening in the tree (I only tested these two paths there might be others). Then we either remove the logging if it serves no purpose (arguable the qiskit.test example falls in this category )or filter the logs from code that is executed on import (the decomposition falls in this example because normally logging the decomposition fidelity can be useful when code is explicitly calling the synthesis routines). Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the celery/celery codebase. Here's the problem: Setting task_compression value doesn't actually do anything ## Checklist * [ ] I have included the output of ``celery -A proj report`` in the issue. (if you are not able to do this, then at least specify the Celery version affected). Celery==4.2.0 * [x] I have verified that the issue exists against the `master` branch of Celery. ## Steps to reproduce ```python3 app = Celery() app.conf.update(task_compression="gzip") ``` ## Expected behavior I would expect that if I set a global `task_compression` config, my tasks are indeed gzipped. I shouldn't have to manually define compression=gzip on each task I want. ## Actual behavior I don't think this setting is respected. This could be the wrong place to look, but it seems like `amqp` is using the wrong compression setting when sending a message: https://github.com/celery/celery/blob/7d9300b3b94399eafb5e40a08a0cdc8b05f896aa/celery/app/amqp.py#L548. `default_compressor` is being set here: https://github.com/celery/celery/blob/7d9300b3b94399eafb5e40a08a0cdc8b05f896aa/celery/app/amqp.py#L483 - should this read `default_compressor = self.app.conf.task_compression` ? Or am I missing something? Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conan-io/conan codebase. Here's the problem: Retry upload for error '500' if the user is requesting it (concurrent uploading) To help us debug your issue please explain: - [ x] I've read the [CONTRIBUTING guide](https://github.com/conan-io/conan/blob/develop/.github/CONTRIBUTING.md). - [ x] I've specified the Conan version, operating system version and any tool that can be relevant. - [ x] I've explained the steps to reproduce the error or the motivation/use case of the question/suggestion. I try to upload a package up to our Artifactory server. We are building for multiple compiler on multiple slaves. Sometimes it happens, that they upload nearly at the same time slot. I thought, that with "--force --retry 5 --retry-wait 10" it would try again to upload again, when this is happening. Unluckily it stops with the first exception happening. [hil_drv_cifx] $ cmd.exe /C "conan upload "*" --all --force --retry 5 --retry-wait 10 -r 9d380644-252b-44ff-b4af-feded185890d --confirm && exit %%ERRORLEVEL%%" ERROR: Error uploading file: conanmanifest.txt, 'b'{\r\n "errors" : [ {\r\n "status" : 500,\r\n "message" : "Failed to persist file with sha1: 3093033974f36098596e33acf477de5a9e8ddd87"\r\n } ]\r\n}'' I am using Conan 1.13.1 on multiple Windows & Linux Jenkins Slaves (all python3.6). We are using the Artifactory plugin for Jenkins (newest version, just some days old) Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: Imports in multiline try blocks are not properly ignored when determining the necessary packages for a modeling file ### System Info - `transformers` version: 4.29.2 - Platform: macOS-13.3.1-arm64-arm-64bit - Python version: 3.10.11 - Huggingface_hub version: 0.14.1 - Safetensors version: not installed - PyTorch version (GPU?): 2.0.1 (False) - Tensorflow version (GPU?): not installed (NA) - Flax version (CPU?/GPU?/TPU?): not installed (NA) - Jax version: not installed - JaxLib version: not installed - Using GPU in script?: N/A - Using distributed or parallel set-up in script?: N/A ### Who can help? @sgugger ### Reproduction The minimal repro is to just call https://github.com/huggingface/transformers/blob/v4.29.2/src/transformers/dynamic_module_utils.py#L118-L134 on a file that has a multiline try import, e.g. ``` try: from package import function from package2 import function except: pass ``` and run the `get_imports` function on it. The output will be `['package', 'package2']`, when it should be `[]` ### Expected behavior Imports in multiline try blocks should be ignored when determining what packages a modeling file requires. I believe https://github.com/huggingface/transformers/blob/ba7054533fa455e8b2dd35feb077e0c7aae646b3/src/transformers/dynamic_module_utils.py#L126 just needs to be modified to include `flags=re.MULTILINE | re.DOTALL`. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: -Db_sanitize=address,undefined doesn't add -fno-omit-frame-pointer Hi, ```python def sanitizer_compile_args(value): if value == 'none': return [] args = ['-fsanitize=' + value] if value == 'address': args.append('-fno-omit-frame-pointer') return args ``` I just noticed that setting `-Db_sanitize=address,undefined` didn't also set `-fno-omit-frame-pointer` for the compile. I believe by not having this, it causes both ubsan and asan to not have good stack traces. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the explosion/spaCy codebase. Here's the problem: Unable to pickle a Token I'm unable to serialize `Token`s. I think this used to work in an earlier version, since I get this exception from a friend's code that used to work fine. I suspect issue #2819 is a manifestation of the same problem, but with Spark wrapping the error message. ## How to reproduce the behavior ``` import spacy, pickle nlp = spacy.load('en') doc = nlp("Hello, world") with open("test_pckl", "wb") as fh: pickle.dump(doc[0], fh) ``` ## Your Environment * **spaCy version:** 2.0.12 * **Platform:** Linux-4.10.0-28-generic-x86_64-with-debian-stretch-sid * **Python version:** 3.6.5 * **Models:** en * **pickleshare version:** 0.7.5 (also tested with 0.7.4) Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: scanbuild.py doesn't handle scan-build-{7,8} Here: https://github.com/mesonbuild/meson/blob/1e7aea65e68a43b0319a4a28908daddfec621548/mesonbuild/scripts/scanbuild.py#L39 As with other LLVM/Clang tools (e.g. `llvm-config`), the version number suffix is just the major component since LLVM 7. The LLVM dependency support handles this correctly here: https://github.com/mesonbuild/meson/blob/54db2c9babe6391bba525f92573ceeadb8303e78/mesonbuild/dependencies/dev.py#L208 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: Datastore: empty lists are not reflected in 'client.put' Related to https://github.com/googleapis/google-cloud-python/pull/3767 Currently, Sending an empty array results in the field not being set. ```python from google.cloud import datastore ds = datastore.Client() key = ds.key('Test') entity = datastore.Entity(key=key) entity['children'] = [] ds.put(entity) print(entity) value = ds.get(entity.key) print(value) key = ds.key('Test') entity = datastore.Entity(key=key) entity['children'] = ['A'] ds.put(entity) print(entity) value = ds.get(entity.key) print(value) ``` Output: ``` <Entity('Test', 5707090131681280) {'children': []}> <Entity('Test', 5707090131681280) {}> <Entity('Test', 5682274280407040) {'children': ['A']}> <Entity('Test', 5682274280407040) {'children': ['A']}> ``` Datastore: empty lists are not reflected in 'client.put' Related to https://github.com/googleapis/google-cloud-python/pull/3767 Currently, Sending an empty array results in the field not being set. ```python from google.cloud import datastore ds = datastore.Client() key = ds.key('Test') entity = datastore.Entity(key=key) entity['children'] = [] ds.put(entity) print(entity) value = ds.get(entity.key) print(value) key = ds.key('Test') entity = datastore.Entity(key=key) entity['children'] = ['A'] ds.put(entity) print(entity) value = ds.get(entity.key) print(value) ``` Output: ``` <Entity('Test', 5707090131681280) {'children': []}> <Entity('Test', 5707090131681280) {}> <Entity('Test', 5682274280407040) {'children': ['A']}> <Entity('Test', 5682274280407040) {'children': ['A']}> ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the google/jax codebase. Here's the problem: Higher order derivatives return wrong results When trying to compute higher order derivatives of a very simple function: ```python def inv(x): return 1/X print(grad(grad(grad(grad(grad(grad(inv))))))(4.)) ``` It prints `-1.9560547` instead of the correct `0.0439453125`. It starts returning incorrect results at 4. It still gets it right with 3.999 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: Update COPYING.txt [From the dev meeting, March 20, 2014](https://hackpad.com/2014-IPython-Weekly-Development-Meetings-v8bNV6EmqVd#:h=March-20,-2014) We should use this header or something similar for source files: ``` python # Copyright (c) IPython Development Team. # Distributed under the terms of the Modified BSD License. ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: Install Sphinx extensions For what seems like a long time now, but matplotlib and IPython have both included `ipython_console_highlighting.py` and `ipython_directive.py`. (I think I wrote the former and John Hunter wrote the latter, originally). Over time, these extensions have diverged. I think the IPython ones are better maintained as they actually track changes to IPython etc., and logically, I think these belong in IPython and not in matplotlib. Unfortunately for third-party users of these packages, IPython does not install the sphinx extensions, but merely keeps them in the source tree. This has encouraged a lot of people to rely on the copies in matplotlib (which are installed). Any chance IPython could install them, too, then we could properly deprecate the copies in matplotlib? Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: `python.extension_module()` linking with libpython when it should not Since version 0.63.0 Meson automatically adds a dependency on libpython when needed compiling extension modules. To determine whether to link to libpython Meson consults `distutils`. On Python 3.7 on Linux, `distutils` says that libpython should not be linked: ```python >>> import distutils.core >>> cmd = distutils.core.Distribution().get_command_obj('build_ext') >>> cmd.ensure_finalized() >>> cmd.get_libraries(distutils.core.Extension('dummy', [])) [] ``` However, the `pkg-config` file for python contains these linker arguments ``` $ pkg-config python3 --libs -L/opt/_internal/cpython-3.7.15/lib -lpython3.7m ``` This code https://github.com/mesonbuild/meson/blob/fd43842041e8ca83b1baee94f053c814e144f98b/mesonbuild/modules/python.py#L524-L543 deals with adding the libpython dependency as need. In the case the libpython dependency is explicitly requested, only the compile arguments are used, however, in the case when it is not explicitly requested, all the arguments are added, including the link arguments found via `pkg-config`. I think that only the compile arguments should be included in this case too when the extension module should not be linked with libpython. I'll prepare a PR, but I would like to check with @eli-schwartz if he agrees on the diagnosis. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conan-io/conan codebase. Here's the problem: [bug] get_cpus is not supporting cgroup2 The current detection of https://github.com/conan-io/conan/blob/1.46.2/conans/client/tools/oss.py#L36-L39 seems no longer applicable in case of cgroup2 as the `/sys/fs/cgroup/cpu/cpu.cfs_quota_us` and `/sys/fs/cgroup/cpu/cpu.cfs_period_us` are replaced by `/sys/fs/cgroup/cpu.max` (in case of docker executed with `--cpus`). There could be checked if cgroup2 is active for example by checking for existence of `/sys/fs/cgroup/cgroup.controllers` file and based on that the values for `quota` and `period` could be taken from `cpu.max` file. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: Explore using coveralls [Coveralls](https://coveralls.io/) is a service for hosting coverage reports of repositories. We currently create a custom website for displaying our coverage here: https://github.com/PrefectHQ/prefect/blob/master/docs/generate_docs.py#L259 and hosted here: https://docs.prefect.io/api/unreleased/coverage.html This is fine, but routinely causes warnings in our netlify builds. In addition to not having to maintain this custom code anymore, we could gain: - tracking our coverage _across time_ - a nice badge prominently displaying our coverage numbers - the ability to merge coverage reports across different runs (this is important for tracking coverage across many task library tasks which are tested in different CI jobs, e.g., `AirflowTask`) Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: Running `run_ner_no_trainer.py` with `--label_all_tokens` falsifies seqeval results ## Environment info - `transformers` version: 4.11.3 - Platform: Linux-5.4.0-80-generic-x86_64-with-glibc2.17 - Python version: 3.8.11 - PyTorch version (GPU?): 1.9.0 (True) - Tensorflow version (GPU?): not installed (NA) - Flax version (CPU?/GPU?/TPU?): not installed (NA) - Jax version: not installed - JaxLib version: not installed - Using GPU in script?: True - Using distributed or parallel set-up in script?: False ## Who can help Examples: - maintained examples (not research project or legacy): @sgugger, @patil-suraj ## Description Hi 🤗 team, not really an bug report, as the code is doing what it should, but not strictly a feature request either. When running `run_ner_no_trainer.py` with `--label_all_tokens`, evaluating with `seqeval` (as default in the script) completely fudges the results. This is due to the fact that `seqeval` is entity based, which means that each sub-token in a "B-" labelled word will be considered as a single entity. Example : Before tokenisation: ``` O B-PERS I-PERS I-PERS The Australian Prime minister ``` -> Number of entities: 1 After tokenisation with `label_all_tokens`: ``` O B-PERS B-PERS I-PERS I-PERS The Austral ##ian Prime minister ``` -> Number of entities: 2 This can yield pretty important differences which may easily be overseen. I think it is worth adding a warning when using the script with this configuration. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conan-io/conan codebase. Here's the problem: [question] profile search order From some testing, it seems conan tries to resolve relative paths to profiles in the following order: 1. resolve from `.conan/profiles` 2. resolve from current directory I'm a bit confused why this order was chosen, as it doesn't seem to be intuitive: Why try the more general solution before the more specific one? --- I stumbled upon this when developing some profiles to later be shared and used with `conan config install`. One referenced profile from the local directory structure (path scheme: `../profiles/xyz`) caused some confusion, as there was another profile installed at `.conan/profiles/xyz` and the latter was chosen instead. [question] profile search order From some testing, it seems conan tries to resolve relative paths to profiles in the following order: 1. resolve from `.conan/profiles` 2. resolve from current directory I'm a bit confused why this order was chosen, as it doesn't seem to be intuitive: Why try the more general solution before the more specific one? --- I stumbled upon this when developing some profiles to later be shared and used with `conan config install`. One referenced profile from the local directory structure (path scheme: `../profiles/xyz`) caused some confusion, as there was another profile installed at `.conan/profiles/xyz` and the latter was chosen instead. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: Which language is available for EncoderDecoderModel pre-trained model? Hi, I have a question. From the example code of [EncoderDecoderModel](https://huggingface.co/transformers/model_doc/encoderdecoder.html#transformers.EncoderDecoderModel.forward), pre-trained model 'bert-base-uncased' looks trained by EN-FR sentence pairs. Is pre-trained model for decoder is trained in French? How can I load pre-trained model in EN-EN pair? Am I confusing? ``` from transformers import EncoderDecoderModel, BertTokenizer import torch tokenizer = BertTokenizer.from_pretrained('bert-base-uncased') model = EncoderDecoderModel.from_encoder_decoder_pretrained('bert-base-uncased', 'bert-base-uncased') # initialize Bert2Bert from pre-trained checkpoints # training model.config.decoder_start_token_id = tokenizer.cls_token_id model.config.pad_token_id = tokenizer.pad_token_id model.config.vocab_size = model.config.decoder.vocab_size input_ids = tokenizer("Hello, my dog is cute", return_tensors="pt").input_ids labels = tokenizer("Salut, mon chien est mignon", return_tensors="pt").input_ids outputs = model(input_ids=input_ids, labels=input_ids) loss, logits = outputs.loss, outputs.logits # save and load from pretrained model.save_pretrained("bert2bert") model = EncoderDecoderModel.from_pretrained("bert2bert") # generation generated = model.generate(input_ids, decoder_start_token_id=model.config.decoder.pad_token_id) ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the DataDog/integrations-core codebase. Here's the problem: Add a service check for missing directories ### What does this PR do? Add option to notify on missing directories and avoid throwing an exception ### Motivation [JIRA#1057](https://datadoghq.atlassian.net/browse/AI-1057) ### Additional Notes ### Review checklist (to be filled by reviewers) - [ ] Feature or bugfix MUST have appropriate tests (unit, integration, e2e) - [ ] PR title must be written as a CHANGELOG entry [(see why)](https://github.com/DataDog/integrations-core/blob/master/CONTRIBUTING.md#pull-request-title) - [ ] Files changes must correspond to the primary purpose of the PR as described in the title (small unrelated changes should have their own PR) - [ ] PR must have `changelog/` and `integration/` labels attached Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: There are broken links for source code Broken links here http://googlecloudplatform.github.io/gcloud-python/#/docs/master/gcloud/storage/client/client when clicking to see source code Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the gitpython-developers/GitPython codebase. Here's the problem: line is missing tab separator As I have whined about in #216, I have a few hits into ``` ====================================================================== ERROR: test_base (git.test.test_reflog.TestRefLog) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/yoh/deb/gits/python-git/git/test/test_reflog.py", line 48, in test_base reflog = RefLog.from_file(rlp_master_ro) File "/home/yoh/deb/gits/python-git/git/refs/log.py", line 154, in from_file return cls(filepath) File "/home/yoh/deb/gits/python-git/git/refs/log.py", line 128, in __init__ self._read_from_file() File "/home/yoh/deb/gits/python-git/git/refs/log.py", line 140, in _read_from_file self._deserialize(fmap) File "/home/yoh/deb/gits/python-git/git/refs/log.py", line 289, in _deserialize self.extend(self.iter_entries(stream)) File "/home/yoh/deb/gits/python-git/git/refs/log.py", line 180, in iter_entries yield new_entry(line.strip()) File "/home/yoh/deb/gits/python-git/git/refs/log.py", line 86, in from_line raise ValueError("line is missing tab separator") ValueError: line is missing tab separator ``` ``` (Pdb) print line 0000000000000000000000000000000000000000 609237d8b5a47d5e68babea116712e5d41e8a949 Yaroslav Halchenko <debian@onerussian.com> 1418863256 +0000 ``` in my case it looks like fields are separated by the space. Where tab should have been? ;) I am also a bit confused with 2 in `info, msg = line.split('\t', 2)` since it would result in up to 3 elements in the list, thus might overfill info, msg pair Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the apache/airflow codebase. Here's the problem: Allow to set statement behavior for PostgresOperator ### Body Add the ability to pass parameters like `statement_timeout` from PostgresOperator. https://www.postgresql.org/docs/14/runtime-config-client.html#GUC-STATEMENT-TIMEOUT The goal is to allow to control over specific query rather than setting the parameters on the connection level. ### Committer - [X] I acknowledge that I am a maintainer/committer of the Apache Airflow project. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conda/conda codebase. Here's the problem: TLS does not appear to be verified As far as I can tell conda is just using urllib2 which doesn't verify SSL at all in Python 2.x and in Python 3.x it doesn't do it by default. This means that even recipes which use a https link without a md5 hash there is a simple MITM code execution attack. <!--- @huboard:{"order":158.5,"custom_state":""} --> Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conan-io/conan codebase. Here's the problem: Global short_paths We are trying to standardize Keysight on conan and one of the big problems we are having in DevOps is that of filename too long for MS builds. While we all recognize this to be a Microsoft problem that will never be fixed by them it is not practical for us to have to re-package 3rd party (or in-house) conan packages by adding short_paths=True to every package in our repo. Is there is a global override I am unaware of that forces all packages to using short paths or is this something that may be added in the next release please? We build across a number of targets with a large number of packages and it would become a full time project just linting conanfiles for short_paths. Hoping for an option in conan.config if possible. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the numpy/numpy codebase. Here's the problem: Segmentation fault when trying to convert numpy array to the C array with ctypes Python 2.7.12 Numpy 1.13.0 Here is error reproduction: ``` import numpy as np from ctypes import POINTER, c_float data = np.ascontiguousarray(np.array([1]*10000, dtype=np.float32)/255).ctypes.data_as(POINTER(c_float)) print data.contents.value # ok data = np.ascontiguousarray(np.array([1]*1000000, dtype=np.float32)/255).ctypes.data_as(POINTER(c_float)) print data.contents.value #giving segmentation fault ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the apache/airflow codebase. Here's the problem: Display DAGs dependencies in CLI ### Description Recently, we added [a new DAG dependencies view](https://github.com/apache/airflow/pull/13199) to the webserver. It would be helpful if a similar diagram could also be displayed/generated using the CLI. For now, only [one DAG can be displayed](http://airflow.apache.org/docs/apache-airflow/stable/usage-cli.html#exporting-dag-structure-as-an-image) using CLI. ![image](https://user-images.githubusercontent.com/12058428/137945580-6a33f919-2648-4980-bd2c-b40cfcacc9fe.png) If anyone is interested, I will be happy to help with the review. ### Use case/motivation * Keep parity between CLI and web serwer. * Enable the writing of scripts that use these diagrams, e.g. for attaching in the documentation. ### Related issues https://github.com/apache/airflow/pull/13199/files ### Are you willing to submit a PR? - [ ] Yes I am willing to submit a PR! ### Code of Conduct - [X] I agree to follow this project's [Code of Conduct](https://github.com/apache/airflow/blob/main/CODE_OF_CONDUCT.md) Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: agent start --env CLI option does not parse lists ## Description Currently the `prefect agent start` does not properly parse list arguments due to the assumption that they are of type string. https://github.com/PrefectHQ/prefect/blob/master/src/prefect/cli/agent.py#L189 This means that some configuration options such as `PREFECT__LOGGING__EXTRA_LOGGERS` implemented in #2010 will not be parsed properly. ## Expected Behavior I expect `prefect agent start -e PREFECT__LOGGING__EXTRA_LOGGERS=['my_logger']` to properly interpret the list. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: Notebook menu File -> Download as -> Python should be based on kernelspec Currently in the notebook, there is an option under `File -> Download as... -> Python (.py)`. Of course, the language name and extension should be gotten from the kernelspec, or perhaps CodeMirror. Also, when the file is created, it should use the kernel's begin-comment string (CodeMirror knows that for many languages), should not prepend "# coding: utf-8", and should not convert magics to Python function calls. As a first draft, it could just download the code cells verbatim, skipping the markdown, and save as `NotebookName.LanguageName` (eg, `MyNotebook.Scheme`). Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: mpl circ drawer fails with `idle_wires=False` ### Environment - **Qiskit Terra version**: latest - **Python version**: - **Operating system**: ### What is happening? ```python qc = QuantumCircuit(6, 5) qc.x(5) qc.h(range(6)) qc.cx(range(5),5) qc.h(range(5)) qc.measure(range(5), range(5)) backend = provider.get_backend('ibm_geneva') trans_qc = transpile(qc, backend, optimization_level=3, approximation_degree=0) trans_qc.draw('mpl', idle_wires=False) ``` gives Traceback (most recent call last): Input In [9] in <cell line: 2> trans_qc.draw('mpl', idle_wires=False) File /opt/miniconda3/envs/qiskit/lib/python3.10/site-packages/qiskit/circuit/quantumcircuit.py:1907 in draw return circuit_drawer( File /opt/miniconda3/envs/qiskit/lib/python3.10/site-packages/qiskit/visualization/circuit_visualization.py:231 in circuit_drawer image = _matplotlib_circuit_drawer( File /opt/miniconda3/envs/qiskit/lib/python3.10/site-packages/qiskit/visualization/circuit_visualization.py:601 in _matplotlib_circuit_drawer return qcd.draw(filename) File /opt/miniconda3/envs/qiskit/lib/python3.10/site-packages/qiskit/visualization/matplotlib.py:323 in draw max_anc = self._get_coords(n_lines) File /opt/miniconda3/envs/qiskit/lib/python3.10/site-packages/qiskit/visualization/matplotlib.py:579 in _get_coords q_indxs.append(self._wire_map[qarg]) KeyError: Qubit(QuantumRegister(27, 'q'), 0) ### How can we reproduce the issue? Do above ### What should happen? should not fail ### Any suggestions? _No response_ Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: Prevent creating flows with schedules if the flow has required parameters Flows with required parameters can't be scheduled (because the parameter values aren't known!). It would be nice if users were made aware of this before they submit the flow; otherwise they won't learn until they try to activate scheduling in cloud. Perhaps the new `Client` (in #374) could prevent submitting flows to Cloud if they: 1. Have a Schedule 2. Have `any([p.required for p in flow.parameters()])` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: Error in nbconvert - closing </code> tag is not inserted in HTML under some circumstances Hi folks - I just noticed that under some circumstances, closing tags for <code> blocks aren't applied, which throws off formatting throughout the rest of the notebook. For an example, checkout this notebook that renders fine in IPython Notebook itself, but does not render properly when converted to HTML. (There is a missing </code> just after "pip install python-linkedin" that's near where you'll see that the example titles start to look funky.) Source notebook is included in the URL below as a file checked into GitHub that you can reference as well. http://nbviewer.ipython.org/urls/raw.github.com/ptwobrussell/Mining-the-Social-Web-2nd-Edition/master/ipynb/Chapter%203%20-%20Mining%20LinkedIn.ipynb Thanks Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the apache/airflow codebase. Here's the problem: Support telegram-bot v20+ ### Body Currently our telegram integration uses Telegram v13 telegram-bot library. On 1st of Jan 2023 a new, backwards incompatible version of Telegram-bot has been released : https://pypi.org/project/python-telegram-bot/20.0/#history and at least as reported by MyPy and our test suite test failures, Telegram 20 needs some changes to work: Here is a transition guide that might be helpful. Transition guide is here: https://github.com/python-telegram-bot/python-telegram-bot/wiki/Transition-guide-to-Version-20.0 In the meantime we limit telegram to < 20.0.0 ### Committer - [X] I acknowledge that I am a maintainer/committer of the Apache Airflow project. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the apache/airflow codebase. Here's the problem: Airflow database upgrade fails with "psycopg2.errors.NotNullViolation: column "map_index" of relation "task_instance" contains null value"s ### Apache Airflow version main (development) ### What happened I currently have Airflow 2.2.3 and due to this [issue](https://github.com/apache/airflow/issues/19699) I have tried to upgrade Airflow to this [commit](https://github.com/apache/airflow/commit/14ee831c7ad767e31a3aeccf3edbc519b3b8c923). When I run `airflow db upgrade` I get the following error: ``` INFO [alembic.runtime.migration] Context impl PostgresqlImpl. INFO [alembic.runtime.migration] Will assume transactional DDL. INFO [alembic.runtime.migration] Running upgrade 587bdf053233 -> e655c0453f75, Add TaskMap and map_index on TaskInstance. Traceback (most recent call last): File "/usr/local/lib/python3.7/dist-packages/sqlalchemy/engine/base.py", line 1277, in _execute_context cursor, statement, parameters, context File "/usr/local/lib/python3.7/dist-packages/sqlalchemy/engine/default.py", line 608, in do_execute cursor.execute(statement, parameters) psycopg2.errors.NotNullViolation: column "map_index" of relation "task_instance" contains null values ``` The map_index column was introduced with this [PR](https://github.com/apache/airflow/pull/20286). Could you please advise? ### What you expected to happen _No response_ ### How to reproduce _No response_ ### Operating System Ubuntu 18.04.6 LTS ### Versions of Apache Airflow Providers _No response_ ### Deployment Other ### Deployment details Kubernetes ### Anything else _No response_ ### Are you willing to submit PR? - [ ] Yes I am willing to submit a PR! ### Code of Conduct - [X] I agree to follow this project's [Code of Conduct](https://github.com/apache/airflow/blob/main/CODE_OF_CONDUCT.md) Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: IPython.lib.editorhooks broken on windows The hook that this module installs uses the `pipes` modules' `quote` function to quote the filename to open. Sadly on Windows this function still uses single quote which the shell doesn't understand, instead of double quotes, meaning the hook doesn't work. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the apache/airflow codebase. Here's the problem: Refactor poll_query_status in EMRContainerHook ### Body The goal is to refactor the code so that we can remove this TODO https://github.com/apache/airflow/blob/7640ba4e8ee239d6e2bbf950d53d624b9df93059/airflow/providers/amazon/aws/hooks/emr_containers.py#L174-L176 More information about the concerns can be found on https://github.com/apache/airflow/pull/16766#discussion_r668089559 ### Committer - [X] I acknowledge that I am a maintainer/committer of the Apache Airflow project. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: BigQuery: [magics] if `destination_var` is set and an error occurs, save the QueryJob for further inspection **Is your feature request related to a problem? Please describe.** When an error occurs, it's useful to have a QueryJob object to inspect the errors properties, as well as check for other details about the job that may have caused the failure. At the very least, a job ID is needed if one wants to file a support ticket about the failure. **Describe the solution you'd like** As identified in https://github.com/googleapis/google-cloud-python/pull/9067#pullrequestreview-278337340, when an error occurs with a `%%bigquery` magic, it would be useful to save the query job object for further inspection of the error and the rest of the job. A problem with this is that in successful cases `destination_var` will be a pandas DataFrame, but in failure cases `destination_var` will be a QueryJob object. Since the magics are primarily used interactively, this probably isn't that much of a problem. **Describe alternatives you've considered** Print out the job ID and have the user call `client.get_job()` in order to inspect the object. This does not work in the case of dry run queries, as no job resource is saved in the backend. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conan-io/conan codebase. Here's the problem: [bug] Conan lockfile fails with conan-new example Related to https://github.com/conan-io/conan/issues/10916 (but this is failing only if the `test_package/` folder is there) ### Steps to reproduce ``` $ conan new cmake_lib -d name=hello -d version=0.1 $ conan lock create . --profile:host default --profile:build default --lockfile-out locks/conan.lock $ conan create . --profile:host default --profile:build default --lockfile-out locks/conan.lock ``` The output ends up with: ``` ... hello/0.1 package(): Packaged 1 '.h' file: hello.h hello/0.1 package(): Packaged 1 '.a' file: libhello.a hello/0.1: Package 'e360b62ce00057522e221cfe56714705a46e20e2' created hello/0.1: Created package revision 8a5fc855aa18f358b89e93c34c816656 Package folder /Users/franchuti/.conan2/p/97df3d62d3551803/p Saving lockfile: /Users/franchuti/develop/conan/tttt/locks/conan.lock Traceback (most recent call last): File "/Users/franchuti/develop/conan/conans/cli/cli.py", line 163, in run command.run(self._conan_api, self._commands[command_argument].parser, args[0][1:]) File "/Users/franchuti/develop/conan/conans/cli/command.py", line 157, in run info = self._method(conan_api, parser, *args) File "/Users/franchuti/develop/conan/conans/cli/commands/create.py", line 99, in create lockfile.save(lockfile_out) AttributeError: 'NoneType' object has no attribute 'save' ERROR: 'NoneType' object has no attribute 'save' ``` My profile: ``` [settings] os=Macos arch=x86_64 compiler=apple-clang compiler.version=12.0 compiler.libcxx=libc++ build_type=Release [options] ``` Even if you get rid of the `test_package/` folder, it's failing as well. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: Implement PyTorch and/or TensorFlow sequence classification architectures for causal language models # 🚀 Feature request The architecture `GPT2ForSequenceClassification` was added in #7501 in PyTorch. It would be great to have it in TensorFlow (cf. issues #7622), but it would also be great to have it for other causal models: ~OpenAI GPT~, ~CTRL~ (PR opened @elk-cloner), ~TransfoXL~ (PR opened @spatil6) Below is a list of items to follow to make sure the integration of such an architecture is complete: - Implement `XXXForSequenceClassification` in `modeling_xxx.py` or `TFXXXForSequenceClassification` in `modeling_tf_xxx.py - Test that architecture in `tests/test_modeling_xxx.py` or `tests/test_modeling_tf_xxx.py` - Add that architecture to `__init__.py` and ` docs/source/model_doc/xxx.rst`. Taking a look at the code changes in #7501 would be a good start. A very good first issue to get acquainted with the library and its architectures! Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the docker/compose codebase. Here's the problem: depends_on Should Obey {{ State.Healthcheck.Status }} Before Launching Services Is it possible for the `depends_on` parameter to wait for a service to be in a "Healthy" state before starting services, if a healthcheck exists for the container? At the moment in 1.8.0-rc2 the `depends_on` parameter only verifies that the container is in a running state, via {{ State.Status.running }}. This would allow for better dependency management in docker-compose. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: 'WhisperProcessor' object has no attribute 'as_target_processor' ### System Info - `transformers` version: 4.23.1 - Platform: Linux-5.15.0-48-generic-x86_64-with-glibc2.17 - Python version: 3.8.12 - Huggingface_hub version: 0.10.1 - PyTorch version (GPU?): 1.11.0 (True) - Tensorflow version (GPU?): not installed (NA) - Flax version (CPU?/GPU?/TPU?): not installed (NA) - Jax version: not installed - JaxLib version: not installed - Using GPU in script?: yes - Using distributed or parallel set-up in script?: no ### Who can help? @patrickvonplaten ### Information - [ ] The official example scripts - [X] My own modified scripts ### Tasks - [ ] An officially supported task in the `examples` folder (such as GLUE/SQuAD, ...) - [X] My own task or dataset (give details below) ### Reproduction I'm trying to train a Whisper model, using the WhisperProcessor. As written in the doc of the `__call__` method of the WhisperProcessor, I should have a context processor.as_target_processor() but it seems it doesn't exist. "If used in the context ~WhisperProcessor.as_target_processor this method forwards all its arguments to WhisperTokenizer’s [call()]" Steps to reproduce the bug : ``` target_text = 'this is a test text' processor = WhisperProcessor.from_pretrained('openai/whisper-large') with processor.as_target_processor(): targets = processor(target_text).input_ids ``` ### Expected behavior The `__call__` method of WhisperProcessor instance in the as_target_processor context should give the result of the WhisperTokenizer `__call__`. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conan-io/conan codebase. Here's the problem: [feature] Remove hook checking license, author Right now it is outputing: ``` [HOOK - attribute_checker.py] pre_export(): .... ``` This can be removed from Conan codebase, implemented strictly in conan hooks Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the docker/compose codebase. Here's the problem: Throw an error if you specify an unrecognised option in `fig.yml` It's very easy to type, e.g., `link` instead of `links`. Or, perhaps for the sake of future compatibility, we should special case a few obvious mistakes. Otherwise new fig.ymls won't work with old versions. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: IPython.parallel.Client behavior as iterator Iterating over a Client only works if the engine ids start at 0, resulting in inconsistent behavior: ``` In [1]: from IPython.parallel import Client In [2]: c = Client() In [3]: print c[:] <DirectView [0, 1, 2, 3]> In [4]: for ct in c: ...: print ct ...: <DirectView 0> <DirectView 1> <DirectView 2> <DirectView 3> In [5]: c = Client() In [6]: print c[:] <DirectView [4, 5, 6, 7]> In [7]: for ct in c: ...: print ct ...: In [8]: ``` Whether Client should be an iterator or not, I think it should at least be consistent. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the explosion/spaCy codebase. Here's the problem: Hindi example is broken ``` $ python3 spacy/lang/hi/examples.py File "spacy/lang/hi/examples.py", line 15 "स्वायत्त कार निर्माताओं की ओर बीमा दायित्व रखती है", ^ SyntaxError: invalid character in identifier ``` This is because the whitespace contains U+00A0 (NO-BREAK SPACE) which Python does not understand. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the google/jax codebase. Here's the problem: float16 support Add support for `np.float16`. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the docker/compose codebase. Here's the problem: fig up and attach should exit when processes exit Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Duplicated code in _simulatortools.py and qasm_simulator_py.py ### Informations - **Qiskit Terra version**: 0.6.1 - **Python version**: 3.6.1 - **Operating system**: Darwin 18.0.0 ### The issue While working on #1153, @charlesastaylor found several functions duplicated in `qiskit/backends/aer/_simulatortools.py` and `qiskit//backends/aer/qasm_simulator_py.py` (such as `index1`). This duplication should be removed. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: CompositeGate became unusable - what is the replacement? ### Informations - **Qiskit Terra version**: 0.7 - **Python version**: 3.6.5 - **Operating system**: Linux ### What is the current behavior? Commit 7485ed924126b0861ef94d35eccef2d3532d70bf removed the `CompositeGate.X = X` from the ` qiskit/extensions/simulator/*.py` files. Because of this, CompositeGate is not usable as before. [This code](https://gist.github.com/nelimee/79f54a75371d65a0c00d59af1cebf874) fails at execution with the error ``` Traceback (most recent call last): File "<input>", line 1, in <module> File "<input>", line 74, in crzz File "<input>", line 64, in __init__ AttributeError: 'CRZZGate' object has no attribute 'cu1' ``` ### Steps to reproduce the problem Download [the code](https://gist.github.com/nelimee/79f54a75371d65a0c00d59af1cebf874) and execute it with a version of Qiskit that contains the modifications of 7485ed924126b0861ef94d35eccef2d3532d70bf. ### What is the expected behavior? The CompositeGate should work as before, i.e. be appended to the quantum circuit. ### Suggested solutions 1. Revert the part of 7485ed924126b0861ef94d35eccef2d3532d70bf that removed the lines `CompositeGate.X = X`. 2. **or** Update the main Changelog with this non-documented removal and provide/document an alternative way to create user-defined custom gates. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conan-io/conan codebase. Here's the problem: Conan database is not formerly closed Coming from https://github.com/conan-io/hooks/pull/17#discussion_r251386053 Seems the Conan database is not being closed when a Conan command finishes and this makes some commands raise in some situations. The above links shows a workaround to overcome the issue but this would need a proper fix in Conan itself as this could be also important when using the conan client API. - [x] I've read the [CONTRIBUTING guide](https://github.com/conan-io/conan/blob/develop/.github/CONTRIBUTING.md). - [x] I've specified the Conan version, operating system version and any tool that can be relevant. - [x] I've explained the steps to reproduce the error or the motivation/use case of the question/suggestion. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: Investigate a splatted version of `defaults_from_attrs` Re: https://github.com/PrefectHQ/prefect/pull/673#discussion_r258760363 Currently, `defaults_from_attrs` accepts a _list_ of strings for which kwargs relate to attrs. This is functional, but isn't pretty. Ideally, `defaults_from_attrs` would accept a splatted list, as in the linked comment. A naive implementation of this, however, gets caught in the `SignatureValidator` for Tasks, which doesn't allow the `*args` pattern, so this will require a little meta-programming work. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: The --help output for -D is ambiguous When you run meson --help, it shows the following for -D. -D PROJECTOPTIONS Set project options. That's a little ambiguous because it implies that -D is only needed once to set multiple options but doesn't give any hint of how to set multiple options with one -D switch. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Parameter does not support ufunc à la QASM ### What is the current behavior? In order to emulate the following QASM, `Parameter` needs to apply along with trigonometry. ``` gate my_gate(phi,lambda) q {u1(cos(phi)/2) q;} ``` A possible way, it would be using `sympy` ``` phi = Parameter('phi') circuit.u1(sympy.cos(phi/2), 0) ``` but this raises `CircuitError: 'invalid param type cos in instruction u1'`. Other libraries like `math` and `numpy` require a float-castable parameter. Same applies to the rest of the "QASM ufunc". ### Suggested solutions Probably, the best solution is to extend `Parameter` type with these ufuncs. So the example would look like: ``` phi = Parameter('phi') circuit.u1((phi/2).cos(), 0) ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: For backwards compatibility shouldn't ipywidgets be a dependency of the ipython notebook? I filed this bug with anaconda: https://github.com/ContinuumIO/anaconda-issues/issues/470#issuecomment-147775813 Right now, `conda install ipython-notebook` provides a broken install for a widget backwards compatible IPython 4. You must seperately install `ipywidgets` for things to work fully in a IPython 3 backward compatible way. My suggestion to Continuum was to include `ipywidgets` as a hard dependency of `ipython-notebook` 4. They said this was an upstream issue. It may also affect `pip install ipython[notebook]` but I haven't checked. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: api_core should respect gapic's polling configuration for LROs. See example [here](https://github.com/googleapis/googleapis/blob/master/google/cloud/videointelligence/v1/videointelligence_gapic.yaml#L48-L54) Note that this does not get populated into the `_config.py` module that is output from the generator, so it's likely we'll need to do an update to the generator to specify the parameters when constructing the `Operation` object. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: Empty rpath-link path prevents linking libstdc++ with clang++ under Linux Hi, My meson build fails to link with clang++ on Linux because clang++ doesn't link in libstdc++. This works with autotools, and it works with meson and gcc. The reason seems to be that (for both g++ and clang++) the link command ends with `-Wl,-rpath-link,`. This doesn't bother gcc, but it does bother clang++, probably because `-Wl,-rpath-link,` absorbs the next argument to the linker, which is probably `-lstdc++` or similar. If I remove this or change it to `-Wl,-rpath-link,yo` then it works. Also, if I change ``` args += ['-Wl,-rpath-link,' + lpaths] ``` to ``` if lpaths != '': args += ['-Wl,-rpath-link,' + lpaths] ``` in compilers/compilers.py Does this sound like the right fix? Maybe the test should be for something containing only whitespace. -BenRI Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: matplotlib visualizer should not use transpiler(format='json') We are going to remove the option `format='json'` from the transpiler (see #1129). For that, we need to move the visualizers into the function `get_instractions` introduced in PR #1187. The file `qiskit/tools/visualization//_matplotlib.py` calls `transpiler.transpile_dag(dag_circuit, basis_gates=self._basis, format='json')`. This needs to be removed in favor of `_utils.get_instructions`. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: Convert all GraphQL calls to snake case The Cloud GraphQL API has been refactored to have consistent casing across all queries and mutations, specifically they are all `snake_case` now. While the old `camelCase` routes are still supported to allow for older versions of Core, we should update our casing for the next release to allow us to deprecate them fully. We will want to thoroughly test the changes to make sure all calls remain valid. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Assemble docs not formatted correctly <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues --> ### Information - **Qiskit Terra version**: master - **Python version**: - **Operating system**: ### What is the current behavior? Similar to #3256 <img width="1081" alt="Screen Shot 2019-10-14 at 5 00 39 AM" src="https://user-images.githubusercontent.com/1249193/66766482-312e8b00-ee7c-11e9-8f03-b5da403be38c.png"> ### Steps to reproduce the problem ### What is the expected behavior? ### Suggested solutions Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: Flow visualize optionally color by state For local debugging, it could be useful for `flow.visualize()` to _optionally_ accept a flow state object, which will then be used to try and color the task-nodes (grey if a task state isn't available). This is useful when understanding how / why / if certain triggers / states were propagated as expected. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: Wrapper Kernel -> `do_shutdown` is not called when the Console is shut down. If I start a wrapper kernel as such: `ipython qtconsole --kernel=my_kernel`, and exit the app via the "X" button, `do_shutdown` is called as expected. If I start it as `ipython console --kernel=my_kernel` and exit the app via `Ctrl+D`, `y`, it is not called. This can be seen by installing @takluyver's bash_kernel and typing a few commands, closing the kernel properly, and reopening. When doing this with the `console`, the history is not preserved. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Count constructor crashes when data is empty <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues --> ### Information - **Qiskit Terra version**: 0.15.1 - **Python version**: 3.7.3 - **Operating system**: Mac OS Catalina 10.15.6 ### What is the current behavior? I simply ran a circuit which does not perform any measurements. On the returned results, `get_counts()` crashes because an empty dictionary is passed into the `Count` constructor and the constructor tries to iterate on the empty dictionary. I tried this on an older version, Terra 0.14.2, which instead of `Count` uses `postprocess.format_counts()`, which simply ignores the empty dictionary and returns an empty dictionary in this case. This did not crash. ### Steps to reproduce the problem Run any circuit without calling `measure()`, then try to apply `get_counts()` to the results. ### What is the expected behavior? `get_counts()` should return an empty dictionary (and not crash). ### Suggested solutions A simple check for an empty dictionary in the `Count` constructor would be sufficient, I think. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: Storage: Add opt-in support for raw downloads. Addresses: #6035, #9003, #1724 Now that `google-resumable-media 0.5.0` is [released](https://github.com/googleapis/google-resumable-media-python/pull/111), update the `Blob.download_*` methods to add an optional `raw_download` argument (defaulting to False, for backward compatibility). If passed as `True`, use the appropriate `RawDownload` / `RawChunkedDownload` objects to perform the download. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: builddir not usable if new option is added Create a project. ``` mkdir foo cd foo echo 'int main(){return 0;}' > main.cpp meson init meson build ninja -C build ``` Update project with an option that breaks "meson setup" on your machine. (The real usecase is that you did `git pull`) ``` echo "option('bar_root', type: 'string', value: 'C:\\\\doesnotexist')" > meson_options.txt echo "lib = meson.get_compiler('cpp').find_library('bar', dirs: get_option('bar_root'))" >> meson.build ``` ninja will of course fail to build. ``` $ ninja -C build ninja: Entering directory `build' [0/1] Regenerating build files. The Meson build system Version: 0.47.0.dev1 Source dir: /tmp/foo Build dir: /tmp/foo/build Build type: native build Project name: foo Native C++ compiler: ccache c++ (gcc 7.3.0 "c++ (Ubuntu 7.3.0-16ubuntu3) 7.3.0") Build machine cpu family: x86_64 Build machine cpu: x86_64 meson.build:9:0: ERROR: Search directory C:\doesnotexist is not an absolute path. A full log can be found at /tmp/foo/build/meson-logs/meson-log.txt FAILED: build.ninja /usr/bin/python3 /home/niklas/.local/bin/meson.py --internal regenerate /tmp/foo /tmp/foo/build --backend ninja ninja: error: rebuilding 'build.ninja': subcommand failed ``` It is not possible to set the correct new value: ``` $ meson configure build/ -Dbar_root=/opt/bar Meson configurator encountered an error: ERROR: Unknown option bar_root. ``` This problem would be less annoying if there was a simple way to figure out the original `meson build -D...` command that was run. #3542 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: running meson fails on latest release 0.51.0 i installed meson 0.51.0 64 using the msi installer and when running "meson" as a test i produces this stack trace: Traceback (most recent call last): ``` File "C:\python\lib\site-packages\cx_Freeze\initscripts\__startup__.py", line 14, in run File "C:\python\lib\site-packages\cx_Freeze\initscripts\Console.py", line 26, in run File "meson.py", line 22, in <module> File "C:\python\lib\pathlib.py", line 1109, in resolve File "C:\python\lib\pathlib.py", line 186, in resolve FileNotFoundError: [WinError 2] The system cannot find the file specified: 'meson' ``` i rolled back to version 0.50.1 which worked correctly Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: use js version of nbagg figures for display The display system shows a png of figure objects, even if they are live nbagg figures and can have a live display. This may require changes on the mpl side as well. attn @pelson Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: run_ner.py crashes with RoBERTa because of incorrect sequence length # 🐛 Bug ## Information I'm running `examples/token-classification/run_ner.py` with RoBERTa. An assert statement fails: ``` assert len(input_ids) == max_seq_length AssertionError ``` Looks like the cause is a mismatch between the value of roberta's `tokenizer.num_special_tokens_to_add()` and the number of special tokens that is actually added to the sequence in `utils_ner.py::convert_examples_to_features()`. Specifically, `tokenizer.num_special_tokens_to_add()` is 2 (presumably for `<s>` and `</s>`). However, `convert_examples_to_features()` adds an extra `</s>` token at line 331, in addition to the `<s>` token and first `</s>` token. So the result is that there are three special tokens, and the sequence ends with `</s> </s>`. `convert_examples_to_features()` relies on `num_special_tokens_to_add()` to determine how many content tokens from the sequence to use, but because of the mismatch above, you can end up with a sequence length of 129 even when the sequence length was set to a max of 128. To reproduce this, just follow the instructions at `examples/token-classification/README.md` except use the flag `--model_name_or_path roberta-base`. The problem arises when using: * [x] the official example scripts: (give details below) * [ ] my own modified scripts: (give details below) ## Environment info - `transformers` version: 2.11.0 - Platform: Linux-4.15.0-101-generic-x86_64-with-debian-buster-sid - Python version: 3.6.10 - PyTorch version (GPU?): 1.5.0 (True) - Tensorflow version (GPU?): 2.2.0 (False) - Using GPU in script?: fails in both cases - Using distributed or parallel set-up in script?: no Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the numpy/numpy codebase. Here's the problem: Weird behavior of structured_to_unstructured on non-trivial dtypes With the following helpers: ```python import numpy.lib.recfunctions as rfn def subarray(dt, shape): return np.dtype((dt, shape)) def structured(*dts): return np.dtype([('x{}'.format(i), dt) for i, dt in enumerate(dts)]) def inspect(dt): arr = np.zeros((), dt) ret = rfn.structured_to_unstructured(arr) print(ret.shape, ret.dtype) ``` We can try a bunch of uses of `structured_to_unstructured` (added in #11526): ```python >>> inspect(structured(int, int)) (2,) int32 # obviously ok >>> inspect(structured(int, structured(int, int))) (3,) int32 # nested types are flattened, ok >>> inspect(structured(int, subarray(int, 2))) (3,) int32 # ok: 1 + 2 >>> inspect(structured(int, subarray(int, (2, 2)))) (5,) int32 # ok: 1 + 2*2 ``` Here's where things start to go bad: ```python >>> inspect(structured(subarray(structured(int, int), 3))) (3,) [('x0', '<i4'), ('x1', '<i4')] # bug? ``` ```python >>> inspect(structured(subarray(subarray(int, 2), 2))) (2, 2) int32 # bug ``` ```python >>> inspect(structured(int)) () int32 # bug ``` (#13334) ```python >>> inspect(structured(int, subarray(subarray(int, 2), 2))) TypeError: invalid type promotion ``` ```python >>> inspect(structured()) dts, counts, offsets = zip(*fields) ValueError: not enough values to unpack (expected 3, got 0) ``` A lot of this behavior looks undesirable to me. @ahaldane, which cases were actually intended to be supported? Rather than locking ourselve into some of these weird constucts, we might want to raise an error for anything non-trivial. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Add support for `Expr` values to `SabreSwap` and `SabreLayout` ### What should we add? Our Sabre implementation works by having Python-space pass a stripped-down, minimal version of the data-flow dependencies down to the Rust layer. This involves a step where wires need to be copied into the new data structures. For historical reasons, the way this is currently done is _not_ by inspecting the wires of the `DAGCircuit` data structure, but they are re-inferred from the nodes themselves. The two passes need updating to ensure that any wires implied by the `Expr` values are also taken into account. The work will be almost identical between the two passes. Rather than having special handling for `Expr` values, an alternative implementation may be to infer the data-flow dependencies from the wires in the DAG structure, rather than the nodes. Depends on #10223, #10224, #9419 and #9421. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: convert_tokens_to_string documentation bug The [documentation](https://huggingface.co/transformers/main_classes/tokenizer.html#transformers.PreTrainedTokenizer.convert_tokens_to_string) states that convert_tokens_to_string would convert _a sequence of token ids in a single string._ That is actually not correct as it converts a sequence of tokens. The method that converts a sequence of token ids is the decode method. Documentation: @sgugger convert_tokens_to_string documentation bug The [documentation](https://huggingface.co/transformers/main_classes/tokenizer.html#transformers.PreTrainedTokenizer.convert_tokens_to_string) states that convert_tokens_to_string would convert _a sequence of token ids in a single string._ That is actually not correct as it converts a sequence of tokens. The method that converts a sequence of token ids is the decode method. Documentation: @sgugger Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: making latex_circuit_drawer and matplotlib_circuit_drawer hidden functions. Why do we need these, can't we just give circuit_drawer and option for this with a default to latex. ```python circuit_drawer(circuit, out_put = 'latex') ``` ```python circuit_drawer(circuit, out_put = 'python') ``` Also, why do we need `generate_latex_source` cant it be ```python circuit_drawer(circuit, out_put = 'latex_source') ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the jupyterlab/jupyterlab codebase. Here's the problem: Unpin tornado dependency #6123 rolled back our dependency on `notebook` due to some upstream issues with async kernel starts (or possibly tornado 6). We need to identify and fix these issues before making a release. Edit: we have resolved the immediate issue with notebook in 5.7.8, but issues with tornado 6 remain. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: Problem with Interactive monitoring of a parallel MPI simulation I got the the first notebook here [Interactive monitoring of a parallel MPI simulation with the IPython Notebook](http://nbviewer.ipython.org/github/ipython/ipython/blob/2.x/examples/Parallel%20Computing/Monitoring%20an%20MPI%20Simulation%20-%201.ipynb) working without MPI on a plain Windows 7 workstation. At the end of the notebook, there is the following: ``` %%px --target 0 from IPython.parallel import bind_kernel; bind_kernel() %connect_info ``` But this gives the following error: ``` --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last)<ipython-input-3-5e39de44d31d> in <module>() ----> 1 from IPython.parallel import bind_kernel; bind_kernel() 2 get_ipython().magic(u'connect_info') c:\Python27\lib\site-packages\IPython\parallel\__init__.pyc in bind_kernel(**kwargs) 67 return app.bind_kernel(**kwargs) 68 ---> 69 raise RuntimeError("bind_kernel be called from an IPEngineApp instance") 70 71 RuntimeError: bind_kernel be called from an IPEngineApp instance ``` Note that I'm using IPython version 2.1.0 on windows 7. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Lightning-AI/lightning codebase. Here's the problem: Streamlined UX in saving, loading, continue training. Currently each time I ran the command with the same experiment name, a new version is created and trained from scratch. If I wanted to load back the model to continue training, I have to create a different script, input the path for the previous checkpoints and meta_tags. Proposal: - Start training, input only 1 `log_path` and 1 `experiment_name`. Test_tube data and saved models will be included in the same folder. - In each experiment, default is to create a new model and trained from scratch (current behavior) - If user passed in `--continue-training`, model will load the latest model (not necessarily the best model) from the latest version, then create a new experiment version and continue training from there. - If user passed in `--continue-training--best`, model will load the the best model from the latest version, then create a new experiment version and continue training from there. - If user passed in `--continue-training(--best) --version=X`, auto load the model from version X and start training. In the end, all the path and dir are determined from only the log_path and name of experiment, and default behavior is the same as of now: `python train.py --exp_name=exp1 --....` If user want to change some hyperparams, or start finetuning, they will only need to add: `python train.py --exp_name=exp1 --.... --continue-trainig--best --version=x` What do you think? Happy to discuss more, as I am not sure this is suitable for cluster training or not. I can make a PR if you're interest. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: Return value of get_option('xxxdir') is inconsistent Since we started allowing passing absolute paths to `xxxdir` such as `--libdir`, it is difficult to know whether `get_option('libdir')` will return the full path to `libdir` or just the path relative to `prefix`. Normally this is not a problem because people will use `join_paths([get_option('prefix'), get_option('libdir')])` which will do the right thing when `get_option('libdir')` returns an absolute path. However, there are use-cases where people want to just fetch the value of `libdir` relative to `prefix`. For instance, Gentoo's init system OpenRC installs libraries in `/usr/lib64` and some of its binaries and scripts (which are not accessible to the user) into `/lib64/rc/bin`, `/lib64/rc/sbin`, `/lib64/rc/sbin`, etc. Gentoo does not use a unified `/usr`, so `/usr/lib64` is not the same as `/lib64`. I can imagine that lots of other 'system-level' projects for distros that don't have a unified `/usr` will face this issue. There are examples in GStreamer as well besides "non-unified /usr"; just search for `grep --include=meson.build -re 'get_option.*libdir'` inside [gst-build](https://cgit.freedesktop.org/gstreamer/gst-build/) with the subprojects cloned. Perhaps many of those can be 'fixed' or changed, but people will keep writing build files with these issues. I propose that if `xxxdir` is an absolute path and a subdir of `prefix`, `get_option('xxxdir')` should return the path **relative to `prefix`**. If it is not, only then must it return the absolute path. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conda/conda codebase. Here's the problem: No error generated on non-existent sub-command ``` [root@70a337fa2e68 build_scripts]# conda info active environment : None user config file : /root/.condarc populated config files : /opt/miniconda/.condarc conda version : 4.4.0rc0 conda-build version : 3.0.9 python version : 3.6.1.final.0 base environment : /opt/miniconda (writable) channel URLs : https://conda.anaconda.org/c3i_test/linux-64 https://conda.anaconda.org/c3i_test/noarch https://repo.continuum.io/pkgs/free/linux-64 https://repo.continuum.io/pkgs/free/noarch https://repo.continuum.io/pkgs/r/linux-64 https://repo.continuum.io/pkgs/r/noarch https://repo.continuum.io/pkgs/pro/linux-64 https://repo.continuum.io/pkgs/pro/noarch package cache : /opt/miniconda/pkgs /root/.conda/pkgs envs directories : /opt/miniconda/envs /root/.conda/envs platform : linux-64 user-agent : conda/4.4.0rc0 requests/2.14.2 CPython/3.6.1 Linux/3.10.0-514.el7.x86_64 centos/6.9 glibc/2.12 UID:GID : 0:0 netrc file : None offline mode : False [root@70a337fa2e68 build_scripts]# conda this-is-not-a-subcommand [root@70a337fa2e68 build_scripts]# echo $? 1 ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the google/jax codebase. Here's the problem: [jet] Unable to determine order from zeroseries When `series_in` consists only of `zeroseries`, [this line](https://github.com/google/jax/blob/master/jax/experimental/jet.py#L116) will fail with ` ValueError: not enough values to unpack (expected 1, got 0)`. This occurs when taking jet through `jax.nn.softplus = lambda x: jnp.logaddexp(x, 0)` as we pass one `zeroseries`to `convert_element_type`. We can avoid the error in this case by avoiding this primitive altogether and manually converting the dtype `lambda x: jnp.logaddexp(x, 0.)`, but I think it's better to fix this in general. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the docker/compose codebase. Here's the problem: AttributeError: 'NoneType' object has no attribute 'tobuf' I upgraded to the latest docker version (1.13) for mac os x and when I try to run docker-compose I get the following error: Traceback (most recent call last): File "<string>", line 3, in <module> File "compose/cli/main.py", line 64, in main File "compose/cli/main.py", line 116, in perform_command File "compose/cli/main.py", line 848, in up File "compose/project.py", line 389, in up File "compose/service.py", line 302, in ensure_image_exists File "compose/service.py", line 786, in build File "site-packages/docker/api/build.py", line 139, in build File "site-packages/docker/utils/utils.py", line 105, in tar File "tarfile.py", line 2046, in addfile AttributeError: 'NoneType' object has no attribute 'tobuf' Everything was working fine on all previous versions of docker for osx until this recent upgrade Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: Timeit results does not show -r value ``` In [1]: timeit -o -r7 -n11 1+1 11 loops, average of 7: 33.1 ns +- 8.77 ns per loop (using standard deviation) Out[1]: <TimeitResult : 11 loops, average of 7: 33.1 ns +- 8.77 ns per loop (using standard deviation)> ``` Should show r=7. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conda/conda codebase. Here's the problem: CONDA_CHANNELS environment variable doesn't work fixed with #3390 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: autoreload fails with tensors Reproducing the bug =============== hola.py ``` import torch class Bhai: three_ones = torch.ones(3) pass ``` test.ipynb ``` In[1]: %load_ext autoreload %autoreload 2 In[2]: from hola import * In[3]: # before executing this cell modify something minor (like adding a space) in `hola.py` print("hello") ``` Before executing the third cell modify something minor (like adding a space) in `hola.py`. I get this error ``` [autoreload of hola failed: Traceback (most recent call last): File "/home/sanyam/miniconda3/lib/python3.6/site-packages/IPython/extensions/autoreload.py", line 244, in check superreload(m, reload, self.old_objects) File "/home/sanyam/miniconda3/lib/python3.6/site-packages/IPython/extensions/autoreload.py", line 393, in superreload update_generic(old_obj, new_obj) File "/home/sanyam/miniconda3/lib/python3.6/site-packages/IPython/extensions/autoreload.py", line 330, in update_generic update(a, b) File "/home/sanyam/miniconda3/lib/python3.6/site-packages/IPython/extensions/autoreload.py", line 278, in update_class if old_obj == new_obj: RuntimeError: bool value of Tensor with more than one value is ambiguous ] ``` Can you help me debug this systematically and explain your reasoning?